EWOLUCJA GENOMÓW

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

Wykład 7 – spis treściświat wirusów (?)ewolucja genomów

GENOMIKA GENOMIKA –– badanie struktury i funkcjonowania genombadanie struktury i funkcjonowania genomóóww

GENOMIKA

GENOMIKA STRUKTURALNA

GENOMIKA PORÓWNAWCZA

GENOMIKA FUNKCJONALNA

MAPOWANIE GENOMU: •Mapy genetyczne •Mapy fizyczne

SEKWENCJONOWANIE

• Ewolucja genomów

• Ewolucja genów

• Transkryptomika

•Regulacja transkrypcji

• Proteomika

Structural

genomics Comparative

genomics

Functional

genomics

II znaczenie: =proteomika

strukturalna

Biolog

ia mo

lekula

rna &

bioi

nfor

maty

ka

Major transitions

in

early

evolution

Hipoteza!

Pre-LUCA diversity

Tree of life?

Tree of life?

Tree of life? Forest of life?

Biol

Direct.

2010 Jul 1;5:44.Save the tree of life or get lost in

the

woods.Valas

RE, Bourne

PE.

Biol

Direct.

2009 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.

Proc Natl

Acad

Sci

U S A.

2010 Oct 5;107(40):17252-5.

Eukaryotic

genes

of

archaebacterial origin

are

more

important

than

the

more

numerous

eubacterial

genes, irrespective

of

function.

Cotton

JA, McInerney

JO.

Genome

Biol

Evol.

2010;2:745-56. Epub 2010 Oct

1.

The

tree

and

net components

of prokaryote

evolution.

Puigbò

P, Wolf YI, Koonin

EV.

Rola wirusów. Hipoteza Forterre’a

Świat wirusów. Hipoteza Koonina

Powstanie eukariontów

Geny „informacyjne” –

z archeonów

Geny „operacyjne” –

z bakterii

Powstanie eukariontów

Geny „informacyjne”

–

z archeonówGeny „operacyjne”

–

z bakterii

Początki kodowania białek

T C A G

T

TTT Phe

TTC Phe

TTA Leu

TTG Leu

TCT Ser

TCC Ser

TCA Ser

TCG Ser

TAT Tyr

TAC Tyr

TAA Ochre

TAGAmber

TGT Cys

TGC Cys

TGA Opal

TGG Trp

C

CTT Leu

CTC Leu

CTA Leu

CTG Leu

CCT Pro

CCC Pro

CCA Pro

CCG Pro

CAT His

CAC His

CAA Gln

CAG Gln

CGT Arg

CGC Arg

CGA Arg

CGG Arg

A

ATT Ile

ATC Ile

ACT Thr

ACC Thr

ACA Thr

ACG Thr

AAT Asn

AAC Asn

AAA Lys

AAG Lys

AGT Ser

AGC Ser

AGA Arg

AGG Arg

ATA Ile

ATG Met

G

GTT Val

GTC Val

GTA Val

GTG Val

GCT Ala

GCC Ala

GCA Ala

GCG Ala

GAT Asp

GAC Asp

GAA Glu

GAG Glu

GGT Gly

GGC Gly

GGA Gly

GGG Gly

A/Ala C/Cys D/Asp E/GluF/PheG/Ala H/His I/Ile K/LysL/LeuM/Met N/AsnP/Pro Q/GlnR/ArgS/SerT/ThrV/ValW/TrpY/Tyr

alaninacysteinakwas asparaginowykwas glutaminowy fenyloalaninaglicynahistydynaizoleucynalizynaleucynametioninaasparaginaprolinaglutaminaargininaserynatreoninawalinatryptofan tyrozyna

2-ga pozycja w kodonie

1-sza pozycja w kodonie

KOD GENETYCZNY

stop

stop

stop

Własności kodu genetycznegoTRÓJKOWY

NIEZACHODZĄCY…

A G A C G A C U U …a1 a2 a3

…

A G A C G A C U U …

a1

a2

a3

a4

a5

a6

a7

…

A G A C G A C U U …

a1

a2

a3a4A

B C

Własności kodu genetycznegoTRÓJKOWY

NIEZACHODZĄCY

BEZPRZECINKOWY

JEDNOZNACZNY

KOLINEARNY

G A A G A C C U U G A G …

kolejność

trójek w mRNA

pierwszatrójka

drugatrójka

trzeciatrójka

czwartatrójka

Glu Asp

Leu

Glu kolejność

aminokwasów w białkupierwszyamin.

drugiamin.

trzeciamin.

czwartyamin.

Własności kodu genetycznego

ZDEGENEROWANY

UNIWERSALNY

TrójkaABC

Amin1

TrójkaABA

Amin2

TrójkaCBC

Amin3

TrójkaCBA

Am4 Am5

Trójka TrójkaAAA AAC

Amin3NIEPRAWDA!!

….

Odstępstwa od kodu genetycznegokodon Uniwersalny

kodMitochondria

ssaczeMitochondria drożdżowe

Mitochondria Drosophila

Mitochondria Aspergillus

TGA STOP tryptofan tryptofan tryptofan tryptofan

AGAAGG

arginina STOP arginina seryna arginina

ATA izoleucyna metionina metionina metionina izoleucyna

CTN leucyna leucyna treonina leucyna leucyna

Rozmiar genomu a liczba genów

Syntenia człowiek - mysz

Ewolucja genomów

MutacjeDuplikacje genówRearanżacje

genów

Utrata genówRearanżacje

chromosomalne

Duplikacje genomów...

Poziomy transfer

genów

Duplikacja genomów

DrożdżeRybyKręgowce (2x ?)

Od tetraploidii do diploidii

Kariotyp a genotyp a fenotyp

Kariotyp a genotyp a fenotyp

muntjac

transfer genówtranspozycja

Transpozony:

Pochodzą

od LUCA?

Selfish

DNA?

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.

Transpozycja: replikatywna

lub

konserwatywna

Type of repeat Subtype Approximate number of copies in the human genome

SINEs 1 558 000

Alu 1 090 000

MIR 393 000

MIR3 75 000

LINEs 868 000

LINE-1 516 000

LINE-2 315 000

LINE-3 37 000

LTR elements 443 000

(retrotransposons) ERV class

I 112 000ERV(K) class

II 8000

ERV(L) class

III 83 000

MaLR 240 000

DNA transposons 294 000

hAT 195 000

Tc-1 75 000

PiggyBac 2000

Transpozony

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.

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.

Hipoteza (Koonin, 2006)

The scenario of the origin and evolution of intronsself-splicing introns

since the earliest stages of

life's evolutionnumerous spliceosomal

introns

invading genes of

the emerging eukaryote during eukaryogenesislineage-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.

Ewolucja przez duplikację genów

Ewolucja przez duplikację genów

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.

transformacja

transdukcja

chromosom bakterii

profag

koniugacja

Transfer skopiowanej pojedynczej nici DNA

Rekombinacja z DNA biorcy

Poziomy transfer genów u eukariontów??

: Science. 2007 Sep 21;317(5845):1753-6. Hotopp

et al.Widespread lateral gene transfer from intracellular bacteria to

multicellular eukaryotes.

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.

Widespread lateral gene transfer from intracellular bacteria to

multicellular eukaryotes.

•

found and confirmed transfers into the genomes of 4 insect and 4 nematode species that range from nearly the entire Wolbachia

genome (>1 megabase) to

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.