"Nothing in biology makes sense except in the light of
evolution" Theodosius Dobzhansky (1900-1975) Slide 2 Genomes of
living organisms sequenced between 1995 and 2002 eubacteria
eukaryote Archaea Slide 3 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" Slide 4
Late-Archaean biosphere acc. Nisbet i Sleep (2001) Salt-loving
archaea Hadean S-processing archaea Methanogens (hyperthermophile)
Methanogens (lower T) A R C H A E A B A C T E R I A High-T
fermenters and hydrogen users Anoxygenic green photosynthesizers
Anoxygenic S photosynthesizers and other purple bacteria
Cyanobacteria (oxybenic photosynthesizers) LUCA CO 2 SO 4 CH 4
H2SH2S Hyperthermophiles Sulphate reducers Fermenters Methanogens
Mesophiles Holdfast H2H2 Water Earliest Archaean Mid-early Archaean
Earliest Archaean Mid-early Archaean Hyperthermophile biofilms and
mats Slide 5 Tree and timescale of life acc. S. B. Hedges, 2002
Eubacteria (Bacteria) Eukaryotes (Eukarya) Archaebacteria (Archaea)
CyApPlAnFu PsAm Mi Eu 0 1 2 3 4 Billion years ago Last common
ancestor Origin of life Eubacteria (Bacteria) Eukaryotes (Eukarya)
Archaebacteria (Archaea) 0 1 2 3 4 Billion years ago Last common
ancestor Origin of life CyApPlAn, Fu Ps Mi Eu? Am? 1.0 D.
melanogaster 1.15 C. elegans 1.55 A. thaliana, S. cerevisiae 2.6 E.
coli, 3.8 Methanobacterium thermoautotrophicum An early 1990s view
The 2002 view Slide 6 Understanding 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. Slide 7 Exon shuffling: An example of
ancestral triosephosphate isomerase (2) Progenote acc. W. Gilbert
et al. (1986) 1500 1000500 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 Slide 8 Exon shuffling: An example of ancestral
triosephosphate isomerase (1) Three dimentional structure of the
enzyme with: coils -helices, arrows -sheets acc. W. Gilbert et al.
(1986) 13 cys 14 asn met 13 38 glu glu 38 78 ser ser 78 107 glu 108
phe glu 107 phe 108 glu 107 leu 108 glu 132 glu 133 asp 152 152 glu
trp 169 gln 180 ala 181 183 glu 184 val gly 210 210 gly 237 lys 238
pro phe 240 COOH NH 2 B. Comparison of proteins sequences of maize,
chicken and the fungus Aspergillus A. COOH NH 2 Slide 9 Segmentally
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. Slide 10
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. Slide 11 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). Slide 12 Nod
gene activation BACTEROID N Fixation 2 NH 4 + N 2 Malate Sucrose
HOST CELL GlutamineAsparagine Root hair cell Rhizobia Infection
thread (invagination of root hair cell membrane) Symbiosome
membrane Rhizobia enter the root cortex cell through the infection
thread Matabolism of infected cells in a root nodule. Glutamine and
asparagine are the main products of N 2 -fixation Symbiotic
interaction between legume and nodule-forming rhizobia Infected
cell Slide 13 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
Slide 14 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 7-9 4-6 0 Lemuriformes Lorisiformes Galago Tarsiiformes
Tarsilus Platyrrhini Cebus Cercopithecinae Colobinae Macaca
Hylobatidae Hylobates Symphalangus Pongidae Pongo Hominidae Gorilla
Pan Homo Mya Cercopithecoidea Hominoidea Catarrhini Simiiformes
Haplorhini Slide 15 Birth of "human-specific" genes important for
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.
