Transcript Slajd 1

Early times
What is life?
Reproduction
Energy transfer
Metabolism
Growth
Life
Homeostasis
A self replicating robot
Evolution
The ability to evolve is an essential feature of life
Did life evolved once?
uses only L-optical isomeres of amino acids
uses the same 20 standard amino acids
uses the same 4 nucleotids
has appr. 20% of genes in common. These represent the genes of basic cell
metabolism.
But
The detailed mechanics of DNA replication are very different between
Archaea and Eubacteria.
Many biochemical pathways are catalysed by non-homologous enzymes.
Today’s basic energy pathway, fermentation, evolved twice in Archaea
and Eubacteria.
Cell membranes and cell walls are non-homologous in Archaea and
Eubacteria.
Archaea and Eubacteria possibly emerged twice.
Some older theories
Primordial soup
Stanley A. Miller
(1930-2007)
Hypercycles
E1
RNA2
E2
RNA1
RNA3
E5
RNA5
E3
RNA4
E4
Panspermia
The hypercycle theory
starts with lipid
bubbles (coacervates)
and replicators that
generate proteins that
assemble other
replicators in a cycle.
Alexandr Oparin
(1894-1980)
Manfred Eigen
(1927-
holds that live first originated in stellar clouds (maybe by using
radioactivity as energy source as found in deep (3 km) rocks on
earth: low diversity Archean communities).
Comets broad life to earth.
The origin of life
Günther
Wächtershäuser
(1938-
Jack Szostak
(1952-
Michael Russel
Bill Martin (1957-
The recent mainstream theory sees basic biochemical reactions prior
to the evolution of replicators.and cell membranes.
First organisms were part of rock surface structures
1. Prebiotic conditions in a medium hot environment powered by a temperature
and pH gradient resulted in the creation of the necessary biomolecules
(monomers).
2. Polymerization of nucleotides resulted in first random replicating RNA that
served also as enzyme.
3. Polymers became enclosed in lipid layers.
4. Evolution set in. Proteins outcompeted ribozymes in catalytic ability.
The distribution of hydrothermal vents on earth
Fornay and Shank, Woods Hole
At Lost City a main process of H2 production is serpentinization of Olivine:
6(Mg1.5,Fe0.5)2 SiO4 + 7H2O → 3[Mg3Si2O5(OH)4] + Fe3O4 + H2
Magnetit Hydrogen
Serpentine
Water
Olivine
Black hydrothermal smokers have core temperatures > 300° C.
Tube worms (Pogonophora)
Cooling deep sea
volcanoes
From Martin et al. 2008
Deep-sea hydrothermal vents support extraordinary diverse ecosystems .
These are the only communities on Earth whose immediate energy source is not
sunlight.
Lost city
Alkaline hydrothermal smokers with core temperatures from 50 to 150° C.
A field of alkaline low temperature
deep sea smokers discovered in
2000.
60 smokers, 10-60 m high.
Carbonate covered.
Inorganic methane and H2
production.
Fe, S-microbubbles in a Lost
City smoker.
Water percolates upward
through the bubbles.
Alkaline smokers
Along slow-spreading systems.
Volcanic heat not required
Exothermic mantle temperatures < 150° C.
Fluids are enriched in CH4, H2, few metals & S
pH 9-11
Support diverse microbial communities, sparse
macrofauna?
Black smokers
Found on all spreading centers
Fueled by cooling volcanoes
Temperatures > 300 C°
Fluids are enriched in CO2, H2S, CH4, H2+metals
pH 2-5
Supports dense and diverse macro-faunal and
microbial communities
The alkaline smoker system
Water percolates downward
into newly formed rocks
Olivine
(Magnesium
Iron Silicate)
and other
minerals
Water percolates upward
forming small bubbles
H2, N2,
H2O, NH3,
CO2, H2S
Serpentinization
Hydrogen,
sulphids
Iron
sulphur
bubbles
50 ° C – 100° C
FeS + H2S →
FeS2 + H2
DG = -38.4 kJmol-1
Exergonic reraction
Percolation of
water within a
temperature
gradient
100 ° C – 200° C
Upward flows from the
upper mantle
Several hundred meters
Water percolates upward
forming small bubbles
50 ° C – 100° C
Steady production
of acetyl - thioesters
DG = -121.3 kJmol-1
Exergonic reaction
Iron–sulphur
minerals
catalyze these
reactions
Iron
sulphur
bubbles
H2 + CO2 + H2S →
CH3SH + H2O
H2 + CO2 → CH4,
CH3COOH,
HCOOH
CO2aq + H2 → CnHm + H2O
Percolation of
water within a
temperature
gradient
100 ° C – 200° C
Abiotic hydrocarbonate
production
Proskurowski G. et al. 2008
Iron-sulphur catalysts are still found at the heart of many proteins today.
For instance, Nitrogenase contains as active catalytic centre Iron-MolybdenumSulfur
Water percolates upward forming small bubbles
pH < 5
Alkaline
hydrothermal
vents
pH > 9
Accumulation
in bubbles at
lower
temperatures
Aminoacid and
nucleotid formation
along the gradients
Acetylphosphate-,
Pyrophosphate act
as energy stores
50° C – 100° C
Iron
sulphur
bubbles
Percolation of
water within a
temperature
gradient
100° C – 200° C
The electrochemical gradient between the alkaline vent fluid and the acidic
seawater leads to the spontaneous formation of acetyl phosphate and
pyrophospate, which act just like adenosine triphosphate or ATP, the chemical that
powers living cells.
These molecules drove the formation of amino acids and nucleotides
Thermal currents and diffusion within the vent pores concentrated larger molecules
like nucleotides, driving the formation of RNA and DNA.
First fatty proto-cell membranes
Water percolates upwoard
forming small bubbles
50 ° C – 100° C
pH < 7
Bubble gets
coated by fatty
molecules
Alkanline
hydrothermal
vents
pH > 7
Bubble gets
coated by fatty
molecules
Bubble gets coated
by fatty molecules
Iron
sulphur
bubbles
Percolation of
water within a
temperature
gradient
100 ° C – 200° C
Some protocells started using ATP as well as acetyl phosphate and pyrophosphate.
The production of ATP using energy from the electrochemical gradient is perfected
with the evolution of the enzyme ATP synthetase, found within all life today.
Proto-cell like vesicles made of fatty acids form spontaneously
and encapsulate nucleotids.
Budin et al. 2009.
The RNA world
Current life needs the interplay
of DNA for reproduction and
proteins for metabolism
RNA is able to replicate and to
catalyze biochemical reactions
(ligating and peptide bonding)
Water percolates upward
forming small bubbles
pH < 7
Alkaline
hydrothermal
vents
pH > 7
Biochemical
cycles differ in
stability
Evolution sets in
Eucaryotic RNaseP ribozyme
50° C – 100° C
Iron
sulphur
bubbles
Self replicating
catalytic
oligonucleotids
Nucleotid formation
along gradients
catalyzed by iron-sulphur
minerals
Percolation of
water within a
temperature
gradient
100° C – 200° C
Two origins of prokaryotes
H2
Proton pump
(Chemiosmosis)
e-
Iron
sulphur
bubbles
Proton
pump
H2
H2
e-
e-
4H2 + 2CO2 →
4H2 + CO2 →
CH3COOH + 2H2O
CH4 + 2H2O
Iron
sulphur
bubbles
e-
H2
Methanogenesis
Acetogenesis
Once protocells could generate their own
electrochemical gradient through
chemiosmosis, they were no longer tied to the
vents.
ATP
Cells left the vents on two separate occasions.
ATP
Eubacteria This marks the beginning of life. Archaea
Own
Own
energy
energy
Eukaryota
production
production
Energy gradient
Within hydrothermal
vents
First metabolic
pathways,
Co-factors
Replicators, Enzymes
Differential
survival
Differential
survival
Homeostasis
Homeostasis
Reproduction
Reproduction
Outside hydrothermal vents
Differential
reproduction
rates
Growth
Differential
reproduction
rates
Growth
Standard chemical
Problems
reactions driven by
electrochemical
RNA –DNA interplay?
gradients
Oligonucleotids and
Generation of
proteins need chiral
autonomous
monomers.
electrochemical
Because all bubbles
gradients
eventually decay
Autonomous
differential survival does
chemical cycles
not mean differential
proliferation of
How long do
autonomous cycles.
bubbles
survive?
Full onset of
evolutionary
process
No replicator transfer
between bubbles.
All has to be within one
lucky bubble?
The question of time.
Full life in
common
sense
If fast evolution to life
why only two primordial
domains?
Or do more exist?
Life started at higher temperatures
Reconstruction of
thermooptima of
ancient enzymes
Gouy, Chaussidon.
2008. Nature 451: 635
The archaean strain
121 grows at 121° C.
And at low temperatures?
The atmosphere of Titan, the largest
Saturn moon, likely produces abiotically
all nucleotid bases, some amino acids
and other organic molecules.
Nanons („nanobacteria”)
Calcifying nanoparticles – carbonate precipitates
First identified as causing kidney stones (1988) by
Kajander and Ciftioglu.
They are possibly involved in biomineralization. This is the formation
of inorganic crystalline structures in association with biological
macromolecules. This process is also referred to as calcification.
Nanons have „cell” walls.
They replicate autonomously and grow.
They do not contain nucleotids.
It is highly controversial
whether these particles
are alive.
Probably they are
self replicating
mineral complexes.
Nanobacteria in limestone
Nanobes (10-150 nm)
Nanobacteria
(50-500 nm)
Mycoplasma
genitalium
(300 nm) smallest
known bacterium
Pelagibacter ubique
(500-600 nm)
Mimivirus
(400 nm)
largest known virus
infects Amoeba
Escherichia coli
(2000-6000 nm)
Nanobes
Nanobes are filament like structures that are 20 to
150 nm in diameter.
They were found in 3 km depth in Australia at
temperatures of app. 150º C.
They are made of Carbon, Oxygen and Nitrogen.
They grow at aerobic conditions.
Perhaps they are only organic crystals that grow
like „normal” inorganic crystals.
The Martian meteorite ALH 84001
Whether they are a new form of living organisms is still highly controversial.
Nanobes from Austrian thermal springs
Thermal springs represent a part of a water-circulating process forming a
temperature gradient.
Long filaments
Nanobes form
biofilms
Single Nanobes
Nested filaments
The way of self assembly
Heinen et al. 2007
Replication and error thresholds
Genome sizes decline during selection.
The length N of simple RNA replicator’s (the information content of
a proto genome) is defined by the Eigen equation
s: a measure of
selective superiority
(fitness)
p: the mean
probability of correct
replication of a
nucleotide
z
Manfred Eigen
(1927-
Replicator size N
s
N  ln(
)
1 p
Region of viable systems
Nmin
1-pmin
Error rate per base (1-p)
1-p is therefore the
error rate
Early replicator systems with high copying error rates had only
limited information content
Three domains of life
Terrestrial forms
Cyanobacteria
Deinococcus radiodurans
Actinobacteria
Proteobacteria
Salmonella
Enterobacterium
Pseudomonas
Helicobacter
Rickettsia
Cell wall
Gram positive
Firmicutes
Spirochaetales
2800-3100 Mya
Euryarcheota
Methanobacteriales
Thermoplasmales
Thermococcales
Methanococcales
3500-3700 Mya
Mostly
extremophiles
Crenarcheota
Sulfolobales
Desulforococcales
Nanoarcheota
Nanoarchaeum
Mycoplasma
Bacillus
Staphylococcus
Streptococcus
Actinobacterium
Thermotogales
Aquifex
Thermophiles
3800-4000 Mya
Mitochondria,
Nucleus, 2000-2700 Mya
9+2 cilia,
cytoskeleton, Eukaryota
meiosis
3800-4100 Mya
Root
The oldest remains of life
Archaeoscillatoriopsis
maxima Marble Bar in
Western Australia
3500 Mya.
It might be a
Cyanobacterium
Stromatolites from the
Gunflint Formation,
Ontario, Canada
1900 Mya are remains of
Cyanobacteria
Oldest known sure
eucaryotes
(chlorophytes) from
San Berhardino,
California having
1400 Mya.
Bacterium from Western
Australia, 3500 Mya.
Again it might be a
Cyanobacterium
A major invention: Endosymbiosis
Mitochondrion (own
DNA similar to
Proteobacteria)
Chloroplasts
(own DNA
similar to
Cyanobacteria)
Lynn Margulis (1938-2011)
Zooxanthellae within hermatypic corals and giant clams
Cyanobacteria
„Life did not take over the globe by combat, but by networking”
Lynn Margulis
Symbiosis are species interactions where species live in close association
over a longer time period
Four genomes in one cell
Buchnera aphidicola
Symbiontic
Bacteria
Mitochondria
Lichen: Ascomycetes+Cyanobacteria
Aphid
nucleus
Acyrthosiphon pisum
Photo: J. White, N. Moran
Percent present O2 level
The rise of the oxygen level
100
10
1
0.1
0.01
0.001
0.0001
0.00001
First
Eukaryotes
First
metazoa
Cyanobacteria
-4
-3
-2
-1
Age [bilions of years]
0
After Anbar (2008)
and Frey et al. (2009)
Why did oxygen levels increase?
1. Plate tectonic changed the demands of oxygen to react with volcanic lava
2. Cyanobacteria invented photosynthesis
3. Effective photosynthesis of cyanobacteria within first Eukaryotes
The endosymbiontic model of eukaryote
emergence
Animal
Plastids
Fungi
Nucleus
Mitochondria
Flagellum
Bikont
plant
Unikont
Aerobic
Proteobacterium
Spirochaetes
Archaea
Eocyte
Cyanobacterium
The model assumes
three steps of
endosymbiosis and a
separate formation of the
nucleus.
The eukaryote nucleus is
a compound of an
archaean genome that
joint with a
proteobacterial genome.
The inside – out model starts with ectosymbiontic proteobacteria
Giganthauma karukerense
with proteobacteria
(Baum and Baum 2014)
The inside out model explains the
basic eukaryotic cell structure
(nucleus, mitochondria,
cytoskeleton) in one step by
enlarging the cell volume to
enclose endosymbiontic
proteobacteria.
Baum and Baum 2014, BMC Biology
A major invention: Sex
Sexual reproduction refers to the
union (syngamy) of two genomes
followed later by genome
segregation (reduction).
Sexual reproduction nearly always
includes recombination that is the
reshuffling of alleles.
Sexual reproduction is an
autapomorphy of all eukaryotes
Many eukaryote lineages returned to
asexual reproduction
Andricus spec.
Rotifer
a
In principle sex is disadvantageous because
• Asexual populations
reproduce faster
Sexual Asexual
• Recombination
destroys
advantageous allele
combinations
• Sexual reproduction
needs investment in
gamete production
and growth
Taraxacum
spec.
Most asexual
(parthenogenetic)
species are
phylogenetically young.
Bdelloid Rotifera are an
exception and pose a
theoretical problem.
Why sex?
Adaptation to changing environments
Sexual species
F1
A B C
F2 AB AC BC
Asexual
species
F1
A B C
Mutation
F2 AA BB BC
Sex generates additional genetic
variability.
The adaptational advantage might
counterbalance the costs of sex
DNA repair during meiosis
DNA glycosylase
AP endonuclease
DNA polymerase 1
DNA ligase
Syngamy allows for DNA repair and
therefore reduced replication error
probabilities.
According to the Eigen equation this
allows for larger genome size.
The basic tree of eukaryotic life
Rhodophytes
Vascular plants
Chlorophytes
Glaucophytes
Chloroplasts
Myxomycetes
1.0-1.6 mya
Metazoa
0.8-1.5 gya
Choanoflagellates
Chromalveolatae
(„Diatomea”,
„Ciliatae”)
Discicristates
(„Euglenoidea
”)
1.6-1.8 mya
Cercozoa
(„Foraminifera”)
Excavates
(„Flagellata”, „Amoeba”)
Nucleus
Sex
Fungi
Mitochondria
Root
2.0-2.7 gya
Cavalier-Smith 2002, 2003
Chromalveolata
Plantae
Chromista
Alveolata
Endosymbionts
The basic tree of eukaryotic life
Contains many paraphyletic groups
(grades)
Plastids
Archezoa
Discicristata
Excavata
Metazoa
Euglena
Porifera
Lamblia
Choanozoa
Eumycota
Heliozoa
Cercozoa
Rhizaria
Rhizopoda
Heliozoa
Saccharomyces
Opisthokonta
Apusozoa
No early evolutionary stages of eucaryotes.
Bikonta
2 cilia The problem of missing links.
Unikonta
Ancyromonas
One cilium, nucleus,
cytoskeleton,
80 S ribosomes,
peroxysomes, mitochondria
Mycetozoa
Lobosa
Root
(2.0-2.7 Gya)
Archamoeba
Arcella
Slime mold
Amoebozoa
Today’s reading
Life on Earth: http://www.cbs.dtu.dk/staff/dave/roanoke/bio101.html
http://www.cbs.dtu.dk/staff/dave/roanoke/bio101ch19a.htm
Lane N. 2009. Was our oldest ancestor a proton powered rock. New Scientist 270.
Martin W., Baross J., Kelley D., Russell M. J. 2008. Hydrothermal vents and the origin of life.
Nature Reviews Microbiology 6: 805-814.
Martin W., Russell M. J. 2007. On the origin of biochemistry at an alkaline hydrothermal vent.
Phil.Trans R. Soc Lond. B. 362: 1887-1926.
Eucaryote origins: http://www.bact.wisc.edu/themicrobialworld/origins.html
http://ijs.sgmjournals.org/cgi/content/abstract/52/2/297
Evolution of sex: http://en.wikipedia.org/wiki/Evolution_of_sex
Recombination: http://www.blackwellpublishing.com/trun/artwork/Animations/
Recombination/recombination.html
Meiosis: http://www.johnkyrk.com/meiosis.html
Molecular timescale of evolution in the Proterozoic:
http://evo.bio.psu.edu/hedgeslab/Publications/PDF-files/182.pdf
The origin of metazoa and the fossil record:
http://www.bionet.nsc.ru/live/ppt/Fedonkin_2003.pdf