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
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.
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
Ewolucja genomów
MutacjeDuplikacje genówRearanżacje
genów
Utrata genówRearanżacje
chromosomalne
Duplikacje genomów...
Poziomy transfer
genów
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.
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.
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.
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.
Top Related