Origin of life and biogeological evolution

Philippe Claeys

http://we.vub.ac.be/~dglg/Web/Teaching/Teaching.html

Origin of life a scientific question for sure but also much more...

«It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present. But if (and oh! what a big if!) we could conceive in some warm little pond, with all sorts of ammonia and phosphoric salts, lights, heat, electricity, etc. present, that a protein compound was chemically formed ready to undergo still more complex changes, at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed» (Darwin C.R., letter to J.D. Hooker, [1 February] 1871, in Darwin F., ed., "The Life and Letters of Charles Darwin," [1898], Basic Books: New York NY, Vol. II, 1959, reprint, pp.202-203)

«We never question the origin of kinetic energy, likewise we should get used to the idea that life always existed and that questioning its origin is futile» (Svante Arrhenius, 1909 Nobel Price, Panspermia believer)

«L’Univers n’est pas gros de vie, ni la biosphère de l’homme. Notre numéro est sorti au jeu de Monte Carlo. Quoi d’étonnant à ce que, tel celui qui vient d’y gagner un milliard, nous éprouvions l’étrangeté de notre condition» (Jacques Monod, 1970, Nobel Price Medicine 1965)

«La vie appartient à la trame même de l’Univers. Si elle n’était pas une manifestation obligatoire des propriétés combinatoires de la matière, il eut été absolument impossible qu’elle prenne naissance naturellement» (Christian de Duve, 1990, Nobel Price Medicine 1974)

In the last few years, I have become increasingly interested in the origin and evolution of life. I have written three books, which have been translated in a number of languages: A Guided Tour of the Living Cell (1984); Blueprint for a Cell (1991); and Vital Dust (1995). I plan to devote my remaining years to further probing what, if anything, our growing understanding of life and mind can tell us about the structure and meaning of the universe (Christian de Duve, 1997)

Define life ?Life: common properties of all living being that differentiate them from non-living systems/things.Very basic definition and not very meaningful even if we dare to add C-based

Life: open structured system where chemical reactions take place and that is capable of regulating its exchanges with the environment and to divide itself into two other systems, each with identical properties, not necessarily similar to those of the initial system (Jacques Reisse, 2006).

Life: is an open or continuous phenomena able to decrease its entropy by processing free energy extracted from its environment, life feeds on negative entropy in contradiction to the Second Law of Thermodynamics (What is life ? Erwin Schroedinger, 1944)

What is alive :

Artificial life in the computer ?Virus ?

Eucaryote

Procaryote

Life: 2 basic cell structures

The cell: chemistry & information

The cell: metabolism

Energy sources

= e- acceptor

Life in the universe

Terrestrial Extraterrestrial ?

Traces Origin Limits Solar system Extrasolar Pamspermia

•fossil•sediments•isotopes•organic components•homochirality

•primitive oceans•building blocks•life in test tube

•temperature•salinity•pH•pressure•deep biosphere

•Mars•Europa•Titan•Ganymede

•exoplanets•signature of extrasolar life

•always existed, transfer between planets, comets, dust, etc.

Earth a “special” place

➡ Sun: middle size star implies long life time

➡ Ideal distance from Sun: 3 phases of H2O coexist

➡ Moon stabilizing effect

➡ Large Jupiter shield

Origin of life : facts

Age of the Earth 4.567 Ga

No rock record until 3.8 Ga

Early Earth anoxic atmosphere

First proven unicellular organisms around 2.7 Ga

Microbial life only for ~ 2 Ga

Development of O2 = major pollution for anaerobic organisms, opportunity for the survivors

First multicellular organisms around 1 Ga

3 domains of life http://www.tolweb.org/tree/

Virus ?

Which came first ?

Based on RNA structure in ribosomes

Classic tree of life based on rRNA sequence comparison (Woese 1987)

One of many possible revisions (see Brinkmann & Philippe, 2005)

Tree of life

Position of the root is open question

Concept of LUCALast Universal Common Ancestor or Cenancestor

(Forterre and Philippe 1999)

What did LUCA look like ?

Two approaches :

• Top - down: from current organism to LUCA

• Bottom - up from atoms and molecules to LUCA, pre-biotic chemistry

What did LUCA look like ?

Extrapolation possible Extrapolation

impossibleTop - Down ?

Prebiotic chemistry

20 amino acids, transition from abiotic to RNA world, peptide world,multiple scenario’s

Miller-Urey experiment 1953 (http://www.ucsd.tv/miller-urey/) showed that organic compounds such as AA, which are used to make proteins that are indispensable for

life, could be made easily under atmospheric conditions of Early Earth.

CH4, NH3, H2,

H2O

Production of HCHO, HCN

HCN + NH3 (Strecker reactions)= Adenine, base in RNA & DNA, and ATP

Adenine

Stepwise pre-biotic chemistrywith increasing complexity

1) Synthesis of the building blocks (AA, nucleic bases, nucleotides etc.)

Primordial soup, Miller-Urey experiments: basic chemical components and energy available as pre-requisites

2) Formation of polymers (nucleic acids, peptides..)

Resulting from interactions (random ? catalyst?, activating agents?) between building blocks, repetition to replication capability of polymers

3) Emergence of supra-molecular architectures, first membranes and individual cells

Individualization, self-replication and carrier of information

Stepwise pre-biotic chemistrywith increasing complexity

1) Synthesis of the building blocks (AA, nucleic bases, nucleotides etc.)

Primordial soup, Miller-Urey experiments: basic chemical components and energy available as pre-requisites

2) Formation of polymers (nucleic acids, peptides..)

Resulting from interactions (random ? catalyst?, activating agents?) between building blocks, repetition to replication capability of polymers

3) Emergence of supra-molecular architectures, first membranes and individual cells

Individualization, self-replication and carrier of information

How do random sequence of improbable reactions lead to a self-replicated system?

The peptide worldCO-NH bond forms from amino acids under dehydration conditions

Pre-biotic soup of AA polymerization

Peptide self-replication

Peptide world

Evolution of genetic code + translation

Protein and nucleic acid world

How convert AA sequence into genetic information ?

Peptide double role catalyst + info carrier with peptide nucleic acid equivalent

No trace preserved of old peptide genetic information systemWhy change to nucleic acid base?

The RNA world

Pre-biotic soup of nucleotide synthesis and replication

RNA world

RNA + protein world

RNA + protein + DNA world

Translation apparatus

Evolution of ribonucleotide reductase

Nucleic acids both info storage and catalysts

No pre-biotic pathways to synthesize mononucleotides

Co-evolution peptide - RNA

Prebiotic chemistry of AA + nucleotides

Coded peptide synthesis + nucleic acid replication

Peptide + nucleic acid world

More complex

Several biochemical processes seem compatible with co-evolution scenario: catalytic AA, peptide + AA stereo-selective catalysis (explain homochirality?), bonds AA & tRNAs, some AA involved in both peptide and nucleic acid oligomerization (N-phosphoryl), reaction AA with inorganic PO4--

Early (hypothetical) metabolism

Most primitive cell must have had metabolism for synthesize macromolecule and energy for cellular functions

Present metabolism too complex with various transporters, e- carriers, enzymes, pigments, and genome with protein encoding

Early cell used simpler process to gain E from environment and make macromolecules

No trace preserved of this old / initial process but most likely took place under anoxic conditions

Anoxic photosynthesis or fermentation/respiration too complex: chemolithotroph pathway’s possible for energy source

Chemolithotroph organisms today are also autotroph’s CO2 into Corg. they use complex pathways such as Calvin cycles, which seem complex for early organisms.

Better use already formed organic molecules

- Molecular H2 is an ideal e- donor reduction potential E0’ = -0.42 for 2H+/H2 2e- (E source for procaryots in geothermal and hyperthermophilic ecosystems black smokers, Yellowstone)

- Elemental S is an ideal e- acceptor S/H2S 2e- E0 = -0.28 also commonly used today by procaryots

Early Energy source ?

Madigan et al. 2003

Metabolism will evolve other ways to derive E and use C

Timing and time scales differences

(Bio)Chemical reactions of life < 1 sec.

Generation time: bacteria min. to years multicellular organisms

Ecosystem development / evolution: > 10 - 1000 years

Evolution of species: kyr to Myr

Evolution of planets: > Myr to Gyr

Timing and time scales differences

(Bio)Chemical reactions of life < 1 sec.

Generation time: bacteria min. to years multicellular organisms

Ecosystem development / evolution: > 10 - 1000 years

Evolution of species: kyr to Myr

Evolution of planets: > Myr to Gyr

How long between building blocks to first cell and then to LUCA?

What about environmental conditions ?

When can this start : concept of planet habitability ?