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Ewolucja genów i genomów

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1 Ewolucja genów i genomów

2 Rozmiar genomu Eukaryota
1 pg DNA = 1Gzasad Alexandrium tamarense Około 140 chromosomów 200 pg DNA/komórkę Rośliny do 150 pg Alexandrium tamarense is a photosynthetic dinoflagellate found in coastal and estuarine regions of the world. The genome size is approximately ca. 200 pg/cell with about 143 or 144 chromosomes of unknown sizes (Courtesy Dr. Debashish Bhattacharya, University of Iowa). Though mainly present in cold to cold-temperate waters, it has also been reported in warmer waters. It is haploid except for the sexual stage.

3 Ciągła reorganizacja genomu
Bloki genów zachowane Syntenia genów rzodkiewnika, ziemniaka i winorośli Rearanżacja chromosomów Syntenic blocks between A. thaliana, potato, and V. vinifera (grape) demonstrating a high degree of conserved gene order between these taxa. X Xu et al. Nature 000, 1-7 (2011) doi: /nature10158

4 Kompresja i ekspansja genomu
Białko HTT odpowiedzialne za chorobę Huntingtona 67 eksonów u człowieka i ryby Takifugu Molecular Biology of the Cell. 4th edition. Alberts B, Johnson A, Lewis J, et al. New York: Garland Science; 2002. Copyright © 2002, Bruce Alberts, Alex Figure 7-113Comparison of the genomic sequences of the human and Fugu genes encoding the protein huntingtin Both genes (indicated in red) contain 67 short exons that align in 1:1 correspondence to one another; these exons are connected by curved lines. The human gene is 7.5 times larger than the Fugu gene (180,000 versus 24,000 nucleotide pairs). The size difference is entirely due to larger introns in the human gene. The larger size of the human introns is due in part to the presence of retrotransposons, whose positons are represented by green vertical lines; the Fugu introns lack retrotransposons. In humans, mutation of the huntingtin gene causes Huntington's disease, an inherited neurodegenerative disorder (see p. 362). (Adapted from S. Baxendale et al., Nat. Genet. 10:67–76, 1995.) Corradi N , Slamovits C H Briefings in Functional Genomics 2011;10: © The Author Published by Oxford University Press. All rights reserved. For permissions, please

5 Gęstość intronów w genomach Eukarya
Leiszmania Roy et al. Nature Reviews Genetics 7, 211–221 (March 2006) | doi: /nrg1807

6 Eksonowa teoria genów Walter Gilbert 1987 Elegancka hipoteza
Dystrybucja intronów nie potwierdza jej Tasowanie eksonów głównie u kręgowców Brown TA. Genomes. 2nd edition. Oxford: Wiley-Liss; 2002. Available from:

7 Pochodzenie intronów jądrowych
Być może od intronów grupy II

8 Genom komórkowy i proteomy w przedziałach komórkowych
Cellular genome and subcellular proteomes. A representation of a eukaryote with ∼5000 protein-coding genes in its nuclear genome is shown. Based on work from the yeast S. cerevisiae, the nuclear genes might code for ∼1000 proteins that are targeted to the endoplasmic reticulum to be distributed through the endomembrane system, ∼3000 proteins that would fold in the cytoplasm (although they might then be redistributed to the peroxisomes or nuclear compartment), and ∼1000 proteins that would be directed to mitochondria by virtue of the specific targeting sequences they carry (53, 54). A further set of proteins are coded in the mitochondrial genome and synthesized on mitochondrial ribosomes. P Dolezal et al. Science 2006;313: Published by AAAS

9 Wędrówka genów między przedziałami
Geny akumulują się w jądrze The eukaryotic mitochondrion is derived from a proteobacterial endosymbiotic ancestor but most of the genes that were originally present in this ancestor's genome have been transferred to the nucleus (thick black arrow), with only a small number being retained in the organelle (blue circle). Similarly, most of the genes from the cyanobacterial endosymbiont ancestor of the chloroplast were also transferred to the nucleus (thick black arrow). So, as a result, cytoplasmic organelles are heavily dependent on nuclear genes and import more than 90% of their proteins from the cytoplasm (white arrows). The dotted arrows indicate how DNA of mitochondrial (blue) and chloroplast (green) origin is still being transferred to the nucleus. Chloroplast and nuclear sequences are also found in the mitochondrial genome but little or no promiscuous DNA is located in the chloroplast.

10 Genomy mitochondrialne
Rickettsia bliski krewny mitochondriów Jacoba, Reclinomonas Excavata mają najwięcej genów mitochondrialnych Figure 5. Mitochondrial genome size and coding content across eukaryotes. Length of coding regions of authentic mitochondrial genes (purple), introns, intronic ORFs, phage-like reverse transcriptases and DNA polymerases (blue), and intergenic regions (green). Species as in Figure 4, plus Amoebidium parasiticum (ichthyosporean protist); Jakoba libera (jakobid flagellate); and Chlamydomonas reinhardtii (green alga, chlorophyte).

11 Geny organellarne Geny uciekają z organelli Drobna część została
Fotosynteza i oddychanie Translacja Hipoteza hydrofobowa (ale Rubisco-LSU) Hipoteza CORR (co-location for redox regulation) Notable flaws are, firstly, that not all protein-coding genes encoded in organelles encode hydrophobic proteins, the most obvious example being the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco-LSU) in chloroplasts; and secondly, both mitochondria and chloroplast already import hydrophobic proteins. The mitochondrial carrier family and the light-harvesting protein of the light-harvesting chlorophyll-protein complex are cited examples for mitochondria and chloroplasts, respectively. Similarly, the CORR hypothesis also has some deficiencies. Firstly, redox control has as yet been demonstrated for only a handful of plastid-encoded genes. Secondly, the expression of many nuclear-encoded mitochondrial and chloroplast proteins is under redox control and yet these proteins are not organelle-encoded [33,34]; thus, why only some redox-controlled genes must be organelle-encoded is not explained by CORR. And thirdly, even for the redox-regulated components encoded by chloroplasts, the products are functional only when combined with additional nuclear-encoded subunits; thus, being organelle-encoded does not offer any immediate advantage in terms of protein function.

12 Geny chloroplastowe W genomach chloroplastowych zostały geny kodujące białka położone blisko centrów aktywnych Note that the set of proteins in (b) encompasses primarily such proteins as are close to the photochemically active photosystem cores

13 Ewolucja przez duplikacje genów
Hemoglobina Rodzina białek wiążących tlen Brown TA. Genomes. 2nd edition. Oxford: Wiley-Liss; 2002.

14 Ewolucja przez duplikacje genów
Ohno, Susumu. (1970). Evolution by gene duplication. Nowe geny mogą powstać przez duplikacje DNA RNA od innego organizmu (gatunku)

15 Duplikacja genów Ohno, Susumu. (1970). Evolution by gene duplication.
Jeżeli po obu stronach jakiegoś genu znajdą się identyczne sekwencje to powstaje sytuacja sprzyjająca duplikacji tego genu Brown TA. Genomes. 2nd edition. Oxford: Wiley-Liss; 2002.

16 Duplikacja genów Dzisiejsza wersja.
Figure 1 (a) Classic Ohno model of duplicate gene fates. Mechanisms of duplication and fates of genes are indicated. Thickness of arrows indicate relative frequency of possible fates. (b) Recent theoretical work supports a much more complex m... Richard C Moore , Michael D Purugganan The evolutionary dynamics of plant duplicate genes Current Opinion in Plant Biology Volume 8, Issue

17 Geneza i ewolucja genów homeotycznych
Figure 1 | Genesis and evolution of Hox and ParaHox clusters. A founder ProtoHox-like gene produced, through a series of cis-duplications, an ancestral Hox-like cluster that consisted of the ProtoHox cluster linked to the ancestor of even-skipped homeotic gene (Evx) and mesenchyme homeobox (Meox). Segmental tandem duplications generated a continuous array of primordial ParaHox, Meox, Hox and Evx genes, which was subsequently broken between the posteriori ParaHox gene caudal-type homeobox (Cdx) and the Meox gene (red arrow). Further cis-duplications and evolution by expansion and genome doublings led to the current mammalian complement of extended Hox and ParaHox genes, consisting of four clusters of each cluster type (A–D). A further gene cluster, EHGbox (not shown), exists that consists of gastrulation brain homeobox (Gbx), motor neuron restricted (Mnx) and engrailed (En). This cluster was created by cis-duplication of a founder gene that was probably adjacent to the ProtoHox gene. Colour codes for the four paralogous groups are: Anterior, purple; Group 3, yellow; Central, green; Posterior, red. Gsh, genomic screened homeobox; Xlox, Xenopus laevis homeobox 8. Oliver Hobert & Heiner Westphal  Trends in Genetics:  2/2000  NATURE REVIEWS | GENETICS VOLUME 6 | DECEMBER 2005 | 881 © 2005 Nature Publishing Group

18 Duplikacja i tasowanie domen białkowych

19 Kasetowa budowa białek
Figure 3. Mechanisms of repeat protein gene expansion. Intron-facilitated and intron-independent repeat motif duplication is indicated by horizontal and vertical arrows, respectively. Sequence drift that reduces similarity between duplicated repeat motifs is indicated by changing colors. (a) Genes that have expanded solely from intron-facilitated duplications are composed exclusively of one-repeat exons. (b) Early intron-independent duplication of a single repeat motif followed by intron-facilitated duplication results in genes that contain all two-repeat exons. Sequence drift after intron-independent duplication, but preceding subsequent intron-facilitated duplication creates an alternating pattern of repeat motif similarity. (c) Intron-independent duplication interspersed among intron-facilitated duplications results in clusters of two-repeat exons. (d) Intron-facilitated duplication followed by late intron-independent duplication results in a two-repeat exon within in a run of one-repeat exons. Ankyrins are a family of adaptor proteins that mediate the attachment of integral membrane proteins to the spectrin-actin based membrane cytoskeleton.[2] Ankyrins have binding sites for the beta subunit of spectrin and at least 12 families of integral membrane proteins. Duplikacje domen Niezależne od intronów Zależne od intronów Białko ANK1 z erytrocytów Street et al. (2006) The Role of Introns in Repeat Protein Gene Formation Journal of Molecular Biology 360,

20 Duplikacja i tasowanie domen białkowych
Tasowanie eksonów Tkankowy aktywator plazminogenu Plazminogen EGF Kringle Białka kaskady krzepnięcia krwi. Tkankowy aktywator plazminogenu

21 Kasetowa budowa białek osocza krwi
Białka tPA Czynnik XII HGFA Fibronektyna Domeny K, Kringle P, proteaza E, EGF-podobna Pr, bogata w prolinę F, Fibronektyna typ I (‘finger’) II, Fibronektyna typ II III, Fibronektyna typ III Fig. 3. Schematic representation of the structure of factor XII, tPA, HGFA and fibronectin. Domain architecture of tPA, factor XII, hepatocyte growth factor activator (HGFA) and fibronectin. F, fibronectin type I (‘finger’) domain; E, Epidermal Growth Factor-like domain; II, fibronectin type II domain; III, fibronectin type III domain; Pr, proline-rich region; K, Kringle; P, protease domain. Martijn et al. Physiological responses to protein aggregates: Fibrinolysis, coagulation and inflammation (new roles for old factors) FEBS Letters Volume 583, Issue

22 Poliploidyzacja u roślin
Wielokrotna duplikacja genomu u roślin nasiennych Figure 3 | Ancestral polyploidy events in seed plants and angiosperms. Two ancestral duplications identified by integration of phylogenomic evidence and molecular time clock for land plant evolution. Ovals indicate the generally accepted genome duplications identified in sequenced genomes (see text). The diamond refers to the triplication event probably shared by all core eudicots. Horizontal bars denote confidence regions for ancestral seed plant WGD and ancestral angiosperm WGD, and are drawn to reflect upper and lower bounds of mean estimates from Fig. 2 (more orthogroups) and Supplementary Fig. 5 (more taxa). The photographs provide examples of the reproductive diversity of eudicots (top row, left to right: Arabidopsis thaliana, Aquilegia chrysantha, Cirsium pumilum, Eschscholzia californica), monocots (second row, left to right: Trillium erectum, Bromus kalmii, Arisaema triphyllum, Cypripedium acaule), basal angiosperms (third row, left to right: Amborella trichopoda, Liriodendron tulipifera, Nuphar advena, Aristolochia fimbriata), gymnosperms (fourth row, first and second fromleft:Zamia vazquezii, Pseudotsuga menziesii) and the outgroups Selaginella moellendorfii (vegetative; fourth row, third from left) and Physcomitrella patens (fourth row, right). See Supplementary Table 4 for photo credits. Jiao et al. Ancestral polyploidy in seed plants and angiosperms 5 M AY | V O L | N AT U R E

23 Heksaploidalna pszenica
Prawdopodobnie z udziałem człowieka

24 Syntenia Dwukrotna duplikacja genomu
~58 milionów lat temu i <13 milionów lat temu Po odgałęzieniu, kolejno winorośli i lucerny Microsyntenic genome segments are centred around Medtr3g104510/Medtr1g (Supplementary Table 10), a duplicated region derived from the ~58-Myr-ago WGD event noted in orange. The <13-Myr-ago G. max-specific WGD is coloured yellow. Orthologous/paralogous gene pairs are indicated through use of a common colour. White arrows represent genes with no syntenic homologue(s) in this genome region. Some of these genes may actually have a syntenic sequence in soybean but no corresponding model reported in the current annotation ND Young et al. Nature 000, 1-5 (2011) doi: /nature10625

25 Rozmnażanie bezpłciowe
Głównie Prokaryota, ale też u Eukaryota Skomplikowany cykl komórkowy u Eukaryota homologiczny z podziałem komórkowym bakterii

26 Cykl komórkowy u bakterii
Homologiczne białka cytoszkieletu u Eukaryota i Prokaryota Cały proces można uznać za homologiczny Gitai (2005) The New Bacterial Cell Biology: Moving Parts and Subcellular Architecture. Cell 120, 577–586.

27 Wspólne pochodzenie białek cytoszkieletu
Tubulina i białko FtsZ mają aktywność GTPazy i wspólną domenę białkową Inne homologiczne białka cytoszkieletu bakterii to MreB, ParM i CreS Występują u eubakterii i archeanów FtsZ Tubulina

28 Wspólne pochodzenie białek cytoszkieletu
Struktura drugorzędowa i przyrównanie sekwencji białka FtsZ z M. jannaschii oraz tubulin ze świni Methanocaldococcus jannaschii (formerly Methanococcus jannas chii) is a thermophilic methanogenic archaea in the class Methanococci. Faguy & Doolittle (1998) Cytoskeletal proteins: The evolution of cell division. Current Biology 8, R338 - R341

29 Wspólne pochodzenie cytoszkieletu
Białko FtsZ odpowiada za podział komórki a białko CreS za jej kształt Białko MreB odpowiada za kształt komórki, jej polarność i segregacje materiału genetycznego Ich ekspresja jest zsynchronizowana w czasie i przestrzeni Gitai (2005) Cell 120, 577–586.

30 Płeć i rozmnażanie płciowe
To proces jednokomórkowy Wiele eukariontów rozmnaża się bezpłciowo Powstał u prokariontów i rozwinął się u wczesnych eukariontów zapewne dzięki rekombinacji Daje przewagę ewolucyjną (w większości sytuacji) Kosztuje Wysiłek zlokalizowania i skłonienia partnera Skomplikowanie cyklu komórkowego

31 Płeć Potomstwo niejednakowe genetycznie
Pozwala to na szybsze dostosowanie się populacji do zmiennych warunków otoczenia przez pozbycie się genów szkodliwych i przechowanie lepszych genów na przyszłość One way meiosis generates genetic variability is through the different ways in which maternal and paternal chromosomes are combined in the daughter cells. The number of possible chromosome combinations in the haploid nuclei is potentially very large. In general, the number of possible chromosome combinations is 2n, where n is the number of chromosome pairs. For example, in fruit flies, which have 4 chromosome pairs, the number of possible combinations is 2n, or 16. For humans, with 23 chromosome pairs, there are over 8 million metaphase arrangements. Copyright © Pearson Education, Inc. or its affiliates. All Rights Reserved.

32 Poliploidyzacja Płodne potomstwo

33 Powstawanie nowych chromosomów
Model of the stepwise evolution of the rye B chromosome after segmental genome duplication. (1) Reciprocal translocation of duplicated fragments of the 3R and 7R chromosomes and unbalanced segregation of a small translocation chromosome results in (2) decay of meiotic A–B pairing and the formation of a proto-B. (3) The accumulation of organellar and A chromosome-derived DNA fragments, amplification of B-specific repeats, erosion and inactivation of A-derived genes (Muller's ratchet), and gain of chromosome drive resulted in the B chromosome. Martis M M et al. PNAS 2012;109: ©2012 by National Academy of Sciences


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