EWOLUCJA GENOMÓW. Bioinformatyka, wykład 7 (29.XI.2010) krzysztof_pawlowski@sggw.pl

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1 EWOLUCJA GENOMÓW Bioinformatyka, wykład 7 (29.XI.2010) krzysztof_pawlowski@sggw.pl

2 Wykład 7 spis treści świat wirusów (?) ewolucja genomów

3 GENOMIKA badanie struktury i funkcjonowania genomów GENOMIKA STRUKTURALNA MAPOWANIE GENOMU: Mapy II genetyczne znaczenie: Mapy =proteomika fizyczne strukturalna SEKWENCJONOWANIE GENOMIKA GENOMIKA PORÓWNAWCZA Ewolucja genomów Ewolucja genów Structural genomics Comparative genomics Functional genomics Biologia molekularna & bioinformatyka GENOMIKA FUNKCJONALNA Transkryptomika Regulacja transkrypcji Proteomika

4 Major transitions in early evolution Hipoteza! Pre-LUCA diversity

5 Tree of life?

6 Tree of life?

7 Tree of life? Forest of life?

8 Biol Direct Jul 1;5:44. Savethetreeoflifeorgetlostin the woods. Valas RE, Bourne PE.

9 Biol Direct Sep 29;4:34. Prokaryotic evolution and the tree of life are two different things. Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin- Hall L, Lapointe FJ, Dupré J, Dagan T, Boucher Y, Martin W.

10 Proc Natl Acad Sci U S A Oct 5;107(40): Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. Cotton JA, McInerney JO.

11 Genome Biol Evol. 2010;2: Epub 2010 Oct 1. The tree and net components of prokaryote evolution. Puigbò P, Wolf YI, Koonin EV.

12 Rola wirusów. Hipoteza Forterre a

13 Świat wirusów. Hipoteza Koonina

14 Powstanie eukariontów Geny informacyjne z archeonów Geny operacyjne z bakterii

15 Powstanie eukariontów Geny informacyjne z archeonów Geny operacyjne z bakterii

16 Początki kodowania białek

17 T 1-sza pozycja w kodonie C A G 2-ga pozycja w kodonie T C A G TTT Phe TCT Ser TAT Tyr TGT Cys TTC Phe TCC Ser TAC Tyr TGC Cys TTA Leu TCA Ser TAA Ochre stop TGA Opal stop TTG Leu TCG Ser TAGAmber stop TGG Trp CTT Leu CCT Pro CAT His CGT Arg CTC Leu CCC Pro CAC His CGC Arg CTA Leu CCA Pro CAA Gln CGA Arg CTG Leu CCG Pro CAG Gln CGG Arg ATT Ile ACT Thr AAT Asn AGT Ser ATC Ile ACC Thr AAC Asn AGC Ser ATA Ile ACA Thr AAA Lys AGA Arg ATG Met ACG Thr AAG Lys AGG Arg GTT Val GCT Ala GAT Asp GGT Gly GTC Val GCC Ala GAC Asp GGC Gly GTA Val GCA Ala GAA Glu GGA Gly GTG Val GCG Ala GAG Glu GGG Gly KOD GENETYCZNY A/Ala alanina C/Cys cysteina D/Asp kwas asparaginowy E/Glu kwas glutaminowy F/Phe fenyloalanina G/Ala glicyna H/His histydyna I/Ile izoleucyna K/Lys lizyna L/Leu leucyna M/Met metionina N/Asn asparagina P/Pro prolina Q/Gln glutamina R/Arg arginina S/Ser seryna T/Thr treonina V/Val walina W/Trp tryptofan Y/Tyr tyrozyna

18 Własności kodu genetycznego TRÓJKOWY NIEZACHODZĄCY A G A C G A C U U a 1 a 2 a 3 A G A C G A C U U A B a 3 a 4 a 5 a 6 a 7 C A G A C G A C U U a 4 a 3 a 2 a 1 a 1 a 2

19 Własności kodu genetycznego TRÓJKOWY NIEZACHODZĄCY BEZPRZECINKOWY JEDNOZNACZNY KOLINEARNY pierwsza trójka druga trójka trzecia trójka czwarta trójka G A A G A C C U U G A G kolejność trójek w mrna Glu Asp Leu Glu kolejność aminokwasów w białku pierwszy amin. drugi amin. trzeci amin. czwarty amin.

20 Własności kodu genetycznego. UNIWERSALNY ZDEGENEROWANY Trójka ABC Trójka ABA Trójka CBC Trójka CBA Trójka Trójka AAA AAC Amin1 Amin2 Amin3 Am4 Am5 Amin3 NIEPRAWDA!!

21 Odstępstwa od kodu genetycznego kodon Uniwersalny kod Mitochondria ssacze Mitochondria drożdżowe Mitochondria Drosophila Mitochondria Aspergillus TGA STOP tryptofan tryptofan tryptofan tryptofan AGA AGG arginina STOP arginina seryna arginina ATA izoleucyna metionina metionina metionina izoleucyna CTN leucyna leucyna treonina leucyna leucyna

22 Rozmiar genomu a liczba genów

23 Syntenia człowiek - mysz

24 Ewolucja genomów Mutacje Duplikacje genów Rearanżacje genów Utrata genów Rearanżacje chromosomalne Duplikacje genomów... Poziomy transfer genów

25 Duplikacja genomów Drożdże Ryby Kręgowce (2x?)

26 Od tetraploidii do diploidii

27 Kariotyp a genotyp a fenotyp

28 Kariotyp a genotyp a fenotyp muntjac

29 transfer genów transpozycja Transpozony: Pochodzą od LUCA? Selfish DNA?

30 transpozony DNA transposons that transpose replicatively, the original transposon remaining in place and a new copy appearing elsewhere in the genome; DNA transposons that transpose conservatively, the original transposon moving to a new site by a cut-and-paste process; Retroelements, all of which transpose via an RNA intermediate.

31 Transpozycja: replikatywna lub konserwatywna

32 Transpozony Type of repeat Subtype Approximate number of copies in the human genome SINEs Alu MIR MIR LINEs LINE LINE LINE LTR elements (retrotransposons) ERV class I ERV(K) class II 8000 ERV(L) class III MaLR DNA transposons hat Tc

33 Efekty transpozonów A transposon that inserts itself into a functional gene will most likely disable that gene. After a transposon leaves a gene, the resulting gap will probably not be repaired correctly. Multiple copies of the same sequence, such as Alu sequences can hinder precise chromosomal pairing during mitosis, resulting in unequal crossovers, one of the main reasons for chromosome duplication.

34 Problem intronów i egzonów Introns late' is the hypothesis that introns evolved relatively recently and are gradually accumulating in eukaryotic genomes. Introns early' is the alternative hypothesis, that introns are very ancient and are gradually being lost from eukaryotic genomes.

35 Hipoteza (Koonin, 2006) The scenario of the origin and evolution of introns self-splicing introns since the earliest stages of life's evolution numerous spliceosomal introns invading genes of the emerging eukaryote during eukaryogenesis lineage-specific loss and gain of introns. intron invasion, probably, spawned by the mitochondrial endosymbiont, might have critically contributed to the emergence of the principal features of the eukaryotic cell.

36 Ewolucja przez duplikację genów

37 Ewolucja przez duplikację genów

38 Poziomy transfer genów horizontal (lateral) gene transfer During conjugation two bacteria come into physical contact and one bacterium (the donor) transfers DNA to the second bacterium (the recipient). The transferred DNA can be a copy of some or possibly all of the donor cell's chromosome, or a segment of chromosomal DNA integrated in a plasmid. Transduction involves transfer of a small segment of DNA from donor to recipient via a bacteriophage. During transformation the recipient cell takes up from its environment a fragment of DNA released from a donor cell.

39 transformacja

40

41 transdukcja profag chromosom bakterii

42 koniugacja Transfer skopiowanej pojedynczej nici DNA Rekombinacja z DNA biorcy

43 Widespread Poziomy lateral transfer gene transfer genów from intracellular bacteria to multicellular eukaryotes. u eukariontów?? found and confirmed transfers into the genomes of 4 insect and 4 nematode species that range from : Science Sep 21;317(5845): Hotopp et al. nearly the entire Wolbachia genome (>1 megabase) to Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. short (<500 bp) insertions. potential Wolbachia-to-host transfers were also detected computationally in three additional sequenced insect genomes. some of these inserted Wolbachia genes are transcribed within eukaryotic cells lacking endosymbionts. Therefore, heritable lateral gene transfer occurs into eukaryotic hosts from their prokaryote symbionts, potentially providing a mechanism for acquisition of new genes and functions. Although common among bacteria, lateral gene transfer-the movement of genes between distantly related organisms-is thought to occur only rarely between bacteria and multicellular eukaryotes. However, the presence of endosymbionts, such as Wolbachia pipientis, within some eukaryotic germlines may facilitate bacterial gene transfers to eukaryotic host genomes. We therefore examined host genomes for evidence of gene transfer events from Wolbachia bacteria to their hosts. We found and confirmed transfers into the genomes of four insect and four nematode species that range from nearly the entire Wolbachia genome (>1 megabase) to short (<500 base pairs) insertions. Potential Wolbachia-to-host transfers were also detected computationally in three additional sequenced insect genomes. We also show that some of these inserted Wolbachia genes are transcribed within eukaryotic cells lacking endosymbionts. Therefore, heritable lateral gene transfer occurs into eukaryotic hosts from their prokaryote symbionts, potentially providing a mechanism for acquisition of new genes and functions.