"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.