"nothing in biology makes sense except in the light of evolution"
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"Nothing in biology makes sense except in the light of evolution". Theodosius Dobzhansky (1900-1975). Genomes of living organisms sequenced between 1995 and 2002. eubacteria. eukaryote. Archaea. Molecular search for the Last Universal Common Ancestor (LUCA). - PowerPoint PPT PresentationTRANSCRIPT
"Nothing in biology makes senseexcept in the light of evolution"
"Nothing in biology makes senseexcept in the light of evolution"
Theodosius Dobzhansky (1900-1975)Theodosius Dobzhansky (1900-1975)
Genomes of living organisms sequencedbetween 1995 and 2002Genomes of living organisms sequencedbetween 1995 and 2002
eubacteriaeukaryote
Archaea
Molecular search for the Last Universal Common Ancestor (LUCA)Molecular search for the Last Universal Common Ancestor (LUCA)
Life appeared on the Earth 3.5 to 3.8 x 109 years ago, soon after the planet was formed
(Archean sedimentary rocks).
The first phyla that emerge in the tree of life based on rRNA sequences are hyper-
thermophylic. This led to the hypothesis that the last universal common ancestor (LUCA)
and possibly the original living organism was hyperthermophylic.
What was the nature of such a primordial form? How did the transition from this first
form of life of all extant biological species take place? What was the LUCA gene content?
The computationally- and experimentally-derived (random gene-knockouts) minimal
gene-set might be as low as 250-300 genes. The present estimate suggest that LUCA
genome could have only 500-600 genes.
"All the organic beings that have ever lived on this Earth may be descended from some single primordial form" Charles Darwin: "Origin of Species"
"All the organic beings that have ever lived on this Earth may be descended from some single primordial form" Charles Darwin: "Origin of Species"
Late-Archaean biosphereLate-Archaean biosphereacc. Nisbet i Sleep (2001)
Salt-loving
archaea
Had
ean
S-processing
archaea
Methanogens
(hyperthermophile)
Methanogens
(lower T)A R
C H
A E
AB A C T E R I A
Hig
h-T
ferm
ente
rs
and
hydr
ogen
use
rs
Ano
xyge
nic
gree
n
phot
osyn
thes
izer
s
Ano
xyge
nic
S
phot
osyn
thes
izer
s an
d
othe
r pu
rple
bac
teri
a
Cya
noba
cter
ia(o
xybe
nic
phot
osyn
thes
izer
s)
LUCA
CO2 SO4
CH4 H2S
HyperthermophilesSulphatereducersFermentersMethanogens
Mesophiles
Holdfast
H2
Water
Earliest A
rchaean
Mid-early Archaean
Earliest Archaean
Mid-early Archaean
Hyperthermophilebiofilms and mats
Tree and timescale of lifeTree and timescale of lifeacc. S. B. Hedges, 2002
Eubacteria(Bacteria)
Eukaryotes(Eukarya)
Archaebacteria(Archaea)
Cy Ap Pl An Fu
Ps Am
Mi
Eu
0
1
2
3
4
Bill
ion
yea
rs a
go
Last common ancestor
Origin of life
Eubacteria(Bacteria)
Eukaryotes(Eukarya)
Archaebacteria(Archaea)
0
1
2
3
4
Bill
ion
yea
rs a
go
Last common ancestor
Origin of life
Cy Ap Pl An,Fu
Ps
Mi
Eu?
Am?
1.0 – D. melanogaster 1.15 – C. elegans1.55 – A. thaliana, S. cerevisiae 2.6 – E. coli,3.8 – Methanobacterium thermoautotrophicum
An early 1990s viewAn early 1990s view The 2002 viewThe 2002 view
Understanding basic mechanisms of genetic diversityUnderstanding basic mechanisms of genetic diversity
It is estimated that there are now recognized at least 1.5 million living species of all
organisms on the Earth. There were many more from the beginning of timescale
of life.
The basic mechanisms shaping the evolution of living species are:
exon-shuffling,
polyploidy,
segmental duplication of eukaryotic
chromosomes,
horizontal gene transfer (HGT),
symbiotic and mutualistic associations.
Exon shuffling:An example of ancestral triosephosphate isomerase (2)
Exon shuffling:An example of ancestral triosephosphate isomerase (2)
Progenote
acc. W. Gilbert et al. (1986)acc. W. Gilbert et al. (1986)
1500 1000 500
Millions of years ago
Human (6)
Rabbit
Chicken (6)
Fish
Maize (8)
Budding yeast (0)Aspergillus (5)
E. coli (0)
B. stearothermophilus (0)
C. An evolutionary tree from AA sequence
Exon shuffling: An example of ancestral triosephosphate isomerase (1)Exon shuffling: An example of ancestral triosephosphate isomerase (1)
Three dimentional structureof the enzyme with:coils – α-helices,arrows – β-sheets
acc. W. Gilbert et al. (1986)acc. W. Gilbert et al. (1986)
13cys
14asn
met13
38glu
glu38
78ser
ser78
107glu
108phe
glu 107
phe 108
glu 107
leu 108
glu 132
glu 133
asp152
152glu
trp169
gln 180
ala181
183glu
184val
gly210
210gly
237lys
238pro
phe240
COOHNH2
B. Comparison of proteins sequences of maize, chicken and the fungus Aspergillus
A.
COOHNH2
Segmentally duplicated regions in the Arabidopsis genomeSegmentally duplicated regions in the Arabidopsis genome
Individual chromosomes are presented as horizontal grey bars. Coloured bands connect
corresponding duplicated segments. Duplicated segments in reversed orientation are
connected with twisted coloured bands.
Horizontal gene transfer (HGT) and the origin of species:lessons from bacteria
Horizontal gene transfer (HGT) and the origin of species:lessons from bacteria
In bacteria, HGT is widely recognized as the mechanism responsible for the
widespread distribution of antibiotic resistance genes, gene clusters encoding
biodegradative pathways, pathogenicity and symbiosis determinants.
Massive HGT events occurred ~2 billion years ago, when the Earth changed from
reducing to oxidizing atmosphere.
Bacterial and viral DNA are constantly integrating in the chromosomes of plants
and animals today by conjugation, transformation (T-DNA of A. tumefaciens),
retroviruses and integrative viruses.
Why are the genomes of endosymbiotic bacteria so stable?Why are the genomes of endosymbiotic bacteria so stable?
Bacterial genomes are continuously modified by the gain and loss of genes. HGT is
one of the most important mechanisms of bacterial evolution.
The comparative analysis of endosymbiotic bacterium Buchnera aphidicola (640 kb)
has revealed high genome stability associated with the absence of chromosomal
rearrangements and HGT events during the past 150 million years. The loss of genes
involved in DNA uptake and recombination in the initial stages of endosymbiosis
underlies this stability. By contrast, two strains of E. coli: K-12 and OH 157:H7 with
only 4.5 Myr of divergence, exhibit genomes whose homology is interrupted by
hundreds of DNA segments.
Extensive loss of genes is a general attribute of the evolution of endosymbiotic
bacteria. Genome stability of microsymbionts is responsible for its co-evolution with
the eukaryotic hosts. This is not the case for facultative symbionts whose genomes
are much larger (e.g. rhizobial species symbiotising with legume plants; 4.5 – 7.5
Mb).
BACTEROID
N Fixation2
NH 4
+
N2
Malate
Sucrose
HOST CELL
Glutamine Asparagine
Roothair cell
Rhizobia
Infection thread(invagination ofroot hair cellmembrane)
Symbiosomemembrane
Rhizobia enter the root cortexcell through the infection thread
Matabolism of infected cells in a rootnodule. Glutamine and asparagineare the main products of N2 -fixation
Symbiotic interaction between legume and nodule-forming rhizobia
Infectedcell
Yellow lupine root nodule morphology
Mature lupine root nodules (42 dpi)
Cross – section of lupine nodule (42 dpi)
nodule cortex
bacteroid tissue
meristematic zone
vascular bundle
Primate phylogenetic relationship based on molecular and fossil record analyses
Primate phylogenetic relationship based on molecular and fossil record analyses
Modern humans (Homo sapiens) and chimpanzees (Pan paniscus and Pan troglodytes) are located in the same genus (Homo) with a common ancestor living 4-6 Mya. A divergence 7-9 Mya is accepted for separation of gorilla (Gorilla) and Homo clade. An estimate of 14 Mya for the divergence of orangutan (Pongo) and African Apes. Gibbon lineage divergence took place about 18 Mya. The Old World monkeys (Cercopithecoidea) include many primate species with baboons (Papio), mandrills (Mandrillus) and Cercopitheques (Cercopithecus) mainly found in Africa as well as macaques (Macaca) predominant in Asia. Divergence for Hominoidea and Cerco-pithecoidea was estimed to 25 Mya.
65-85
50-60
35-45
25
18
14
7-94-6
0
LemuriformesLorisiformesGalago
TarsiiformesTarsilus
PlatyrrhiniCebus
CercopithecinaeColobinaeMacaca
HylobatidaeHylobatesSymphalangus
PongidaePongo
HominidaeGorilla Pan
Homo
Mya
Cercopithecoidea Hominoidea
Catarrhini
Simiiformes
Haplorhini
Birth of "human-specific" genes importantfor primate evolution
Birth of "human-specific" genes importantfor primate evolution
Humans and the Great African Apes share very similar chromosome structure and
genomic sequence at the DNA level with 98.5-99% homology (chimpanzee).
What makes us different at the genetic level from the closest relatives - Antropoids?
A recent major breakthrough was identification of "human-specific" genes. Also,
specific chromosomal regions have been mapped that display all the features of
"gene nurseries" and could have played a major role in gene innovation and
speciation during primate evolution.
Two highly conserved human genes were identified (PRM2, histon-like protein
essential to spermatogenesis and FOXP2-transcription factor involved in speech
and language development) which were probably the selection targets in recent
human evolution.