EWOLUCJA GENOMÓW

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EWOLUCJA GENOMÓW
EWOLUCJA GENOMÓW
Bioinformatyka, wykład 7 (29.XI.2010)
krzysztof_pawlowski@sggw.pl
Wykład 7 – spis treści
„
„
świat wirusów (?)
ewolucja genomów
at
or
m
GENOMIKA
yk
a
GENOMIKA –
badanie struktury i funkcjonowania genomów
GENOMIKA
PORÓWNAWCZA
GENOMIKA
FUNKCJONALNA
bi
oi
nf
GENOMIKA
STRUKTURALNA
&
MAPOWANIE GENOMU:
• Ewolucja
• Transkryptomika
•Regulacja transkrypcji
ar
na
•Mapy
IIgenetyczne
znaczenie:
•Mapy
fizyczne
=proteomika
genomów
• Ewolucja genów
ul
strukturalna
ol
ek
SEKWENCJONOWANIE
• Proteomika
Bi
ol
og
ia
m
Structural genomics
Comparative genomics
Functional genomics
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, FranklinHall 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 archeonów
Geny „operacyjne” – z bakterii
Początki kodowania białek
T
1-sza pozycja w kodonie
T
C
A
G
2-ga pozycja w kodonie
C
A
KOD GENETYCZNY
G
TTT Phe
TCT Ser
TAT Tyr
TGT Cys
TTC Phe
TCC Ser
TAC Tyr
TGC Cys
TTA Leu
TCA Ser
stop
TAA Ochre
stop
TGA Opal
TTG Leu
TCG Ser
stop
TAGAmber
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
A/Ala
C/Cys
D/Asp
E/Glu
F/Phe
G/Ala
H/His
I/Ile
K/Lys
L/Leu
M/Met
N/Asn
P/Pro
Q/Gln
R/Arg
S/Ser
T/Thr
V/Val
W/Trp
Y/Tyr
alanina
cysteina
kwas asparaginowy
kwas glutaminowy
fenyloalanina
glicyna
histydyna
izoleucyna
lizyna
leucyna
metionina
asparagina
prolina
glutamina
arginina
seryna
treonina
walina
tryptofan
tyrozyna
Własności kodu genetycznego
TRÓJKOWY
NIEZACHODZĄCY
… A G A C G A C U U …
a1
A
a2
… A G A C G A C U U …
a3
B
a4
a1
a2
a3
a5
a6
a7
… A G A C G A C U U …
C
a1
a2
a3
a4
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 …
Glu
pierwszy
amin.
Asp
drugi
amin.
Leu
trzeci
amin.
Glu
czwarty
amin.
kolejność trójek w mRNA
kolejność aminokwasów w białku
Własności kodu genetycznego
….
UNIWERSALNY
ZDEGENEROWANY
Trójka
ABC
Trójka
ABA
Trójka
CBC
Trójka
CBA
Trójka Trójka
AAA
AAC
Amin1
Amin2
Amin3
Am4 Am5
Amin3
NIEPRAWDA!!
Odstępstwa od kodu genetycznego
kodon Uniwersalny Mitochondria Mitochondria
drożdżowe
kod
ssacze
Mitochondria
Mitochondria
TGA
STOP
tryptofan
tryptofan
tryptofan
tryptofan
AGA
arginina
STOP
arginina
seryna
arginina
ATA
izoleucyna
metionina
metionina
metionina
izoleucyna
CTN
leucyna
leucyna
treonina
leucyna
leucyna
Drosophila
Aspergillus
AGG
Rozmiar genomu a liczba genów
Syntenia człowiek - mysz
Ewolucja genomów
Mutacje
Duplikacje genów
Rearanżacje genów
Utrata genów
Rearanżacje chromosomalne
Duplikacje genomów
...
Poziomy transfer genów
Duplikacja genomów
Drożdże
Ryby
Kręgowce (2x ?)
Od tetraploidii do diploidii
Kariotyp a genotyp a fenotyp
Kariotyp a genotyp a fenotyp
muntjac
transfer genów
transpozycja
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
Transpozony
Subtype
SINEs
1 558 000
Alu
MIR
MIR3
LINEs
1 090 000
393 000
75 000
868 000
LINE-1
516 000
LINE-2
315 000
LINE-3
37 000
LTR elements
(retrotransposons)
Approximate number of copies
in the human genome
443 000
ERV class I
ERV(K) class II
ERV(L) class III
MaLR
DNA transposons
112 000
8000
83 000
240 000
294 000
hAT
195 000
Tc-1
75 000
PiggyBac
2000
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 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.
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
profag
chromosom
bakterii
koniugacja
Transfer
skopiowanej
pojedynczej
nici DNA
Rekombinacja z
DNA biorcy
Poziomy transfer genów
u eukariontów??
• found and confirmed transfers into the genomes
Widespread lateral gene transfer from intracellular
bacteria to multicellular eukaryotes.
of 4 insect and 4 nematode species that range from
Science. 2007 Sep 21;317(5845):1753-6. Hotopp et al.
nearly:Widespread
the entire
Wolbachia genome (>1 megabase) to
lateral gene transfer from intracellular bacteria to
short (<500
bp) insertions.
multicellular
eukaryotes.
• potential
Wolbachia-to-host transfers were also
Although common among bacteria, lateral gene transfer-the movement of genes
distantly related organisms-is
thought
to occursequenced
only rarely
detectedbetween
computationally
in
three
additional
between bacteria and multicellular eukaryotes. However, the presence of
endosymbionts, such as Wolbachia pipientis, within some eukaryotic
insect genomes.
germlines may facilitate bacterial gene transfers to eukaryotic host
genomes.
therefore examined
host genomes
forare
evidence of gene
• some of
theseWeinserted
Wolbachia
genes
transfer events from Wolbachia bacteria to their hosts. We found and
transcribed
within
eukaryotic
cellsoflacking
confirmed
transfers
into the genomes
four insect and four nematode
species that range from nearly the entire Wolbachia genome (>1 megabase)
endosymbionts.
to short (<500 base pairs) insertions. Potential Wolbachia-to-host transfers
were also detected computationally in three additional sequenced insect
• Therefore,
heritable
transfer
occursgenes
intoare
genomes.
We also showlateral
that somegene
of these
inserted Wolbachia
transcribed within eukaryotic cells lacking endosymbionts.
eukaryotic
hosts from their prokaryote symbionts,
Therefore,
heritable lateral
gene transferfor
occurs
into eukaryoticof
hosts
from
potentially
providing
a mechanism
acquisition
new
their prokaryote symbionts, potentially providing a mechanism for
acquisition
of new genes and functions.
genes and
functions.

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