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Open questions and challenges in current research on the origins of life

Kepa Ruiz-Mirazo

SFE Rencontres 2014 La Baule, France, 7th of October, 2014

Dept. of Logic and Philosophy of Science/Biophysics Research Unit (CSIC-UPV/EHU)

«A true understanding of the essential nature of life is only possible in the light of a knowledge

of its origin and [evolutionary] development.»

[Oparin 1961]

400 million years: time window for

the origin of unicellular organisms

2000 million years: time window for the origin of

(unicellular) eukaryote organisms

800 million years: time window for the origin of pluricellular

organisms

ASTROBIOLOGY : pro: POSING THE PROBLEM IN GENERAL and PHYSICO-CHEMICALLY REALISTIC TERMS! con: TOO SIMPLIFIED and OBSOLETE (MOLECULARLY REDUCTIONIST) PICTURE OF BIOLOGICAL COMPLEXITY

DNA or protein ?

Even if RNA ‘self-replication’ is achieved in vitro … … where does RNA come from?

‘ pre-RNA world ’

ORIGINS OF LIFE (i)

~10 million years [Lazcano & Miller 1994]

CELLULAR METABOLISMS

?

PREBIOTIC MOLECULAR EVOLUTION

‘ RNA world ’

→ → MACROMOLECULAR STRUCTURES

‘ RNA -protein world ’

Sequence of chemical pathways leading to biomolecular components :

[Eschenmoser, Benner, Nielsen ...]

Even if the ‘prebiotic synthesis’ of RNA molecules is also achieved in the lab in the near future…

… is that ALL that life requires?

http://www.genome.jp/kegg/pathway/map/map01100.html

Kyoto Encyclopedia of Genes and Genomes (KEGG)

http://www.genome.jp/kegg/pathway/map/map01100.html

Kyoto Encyclopedia of Genes and Genomes (KEGG)

ORGANIZATION THROUGH

SYNTHESIS (not just ‘self-organization’)

[of previously synthesized organic compounds]

KANT (!)

Escherichia coli K12

Buchnera aphidicola Cc

Homo sapiens

LIFE: SYSTEM PROPERTY ! → ORIGINS: SYSTEMIC APPROACH!!

CAPACITY FOR ‘SELF-CONSTRUCTION’

(metabolism)

POTENTIAL FOR ‘INDEFINITE GROWTH OF COMPLEXITY’

(‘Darwinian’ evolution)

‘minimal life’ definition

‘autonomy’ ‘open-ended evolution’

[Ruiz-Mirazo et al. 2004, Origs. Life Evol. Biosph.]

LIFE : very complex molecules (DNA, RNA, proteins, sugars, lipids,...)

very complex organization and dynamics (‘genetically-instructed’ cellular metabolisms)

[Reprinted (2010): Anthology on the nature of life -- CUP]

a UNIVERSAL but also OPERATIONAL definition !

[Ruiz-Mirazo et al. 2004, 2010]

Any living system must include the following components:

a semi-permeable active boundary (i.e., a membrane),

an energy transduction/conversion apparatus (a set of chemical/chemiosmotic energy currencies)

and, at least, two types of interdependent macromolecular components:

some carrying out and coordinating directly self-construction processes (catalysts) and some others storing and transmitting

information which is relevant to carry out efficiently those processes in the course of subsequent generations (records)

Universal biochemical features

DNA as the genetic material

Genetic code

Energy currencies Homochirality

Cellular boundary Common coenzymes and metabolic

intermediaries

(modified from J. Peretó)

ORIGINS OF LIFE (ii) Sequence of transitions that lead to

self-producing systems with potential for open-ended evolution?

:

~10 million years [Lazcano & Miller 1994]

[de Duve, Wächtershäuser, Kauffman,...]

CELLULAR SYSTEMS → (PROTO-)METABOLISMS

[Morowitz, Deamer, Luisi, Szostak ...]

[Koonin, Venter, Moya, Luisi, Lazcano,...]

?

[Szostak, Yomo, Luisi,...]: S-S (in between?) ENERG.

COUPLED REACTION NETWORKS

(with available organic and inorganic

compounds)

B-U T-D

? ?

Forthcoming: EXTENSIVE

REVIEW (Chem. Revs. 2013)

(!!!!!)

‘Infrabiological’ systems

(Szathmáry et al., 2005 )

[Ganti 1975]

«A MODEL SHOULD BE AS SIMPLE AS POSSIBLE, BUT NOT SIMPLER....» Albert Einstein

Is network autocatalysis feasible

within the network of plausible

prebiotic reactions?

Schwartz

Eschenmoser

Sutherland

Pascal

Autocatalytic synthetic loops in prebiotic chemistry ???

[SLIDE: courtesy of A. de la ESCOSURA]

BIOENERGETIC MECHANISMS: CHEMIOSMOSIS

[Lipmann 1941] [Mitchel 1961] [Harold 1986] . . . . [Skulachev 1992]

Skulachev’s (1992) ‘laws of bioenergetics’:

(i) no direct use: conversion to the system’s own currencies,

(ii) which are at least of two types: water soluble & membrane-linked,

(iii) they are interconvertible, so enough if just one is coupled to the external source

ATP

∆ µ H + ∆ µ Na + W W

W

Energy sources (fermentation/glycolytic substrates)

Energy sources (light, respiratory substrates)

W mechanical chemical osmotic

COMPARTMENT (topologically closed & selectively permeable membrane)

CATALYSTS & TRANSPORTERS ENERGY CURRENCIES

.

(functional-metabolic components: in charge of ‘kinetic control’ and

‘spatial control’ tasks) (soluble intermediary compounds &

electro-chemical gradients)

control on boundary conditions (‘agency’)

Autonomous system with open-ended evolutionary capacities

matter-energy (influx)

RECORDS (informational components: template replicators, ‘molecular fixers’ of complexity)

(∆µ*)

matter-energy (outflux)

(Ruiz-Mirazo, K.: PhD dissertation, 2001)

(‘functional integration’) space-temporal coordination

‘basic autonomous’ systems

‘OLIGOMER (peptides) WORLD’

‘hereditary autonomous’ systems

‘ONE-POLYMER (RNA) WORLD’

minimal living systems (autonomy + open-ended evolution):

‘TWO/THREE-POLYMER WORLD’ (RNA-protein/DNA-RNA-protein)

second major ‘bottleneck’: ‘template-replication’ mechanisms

third major bottleneck: phenotype-genotype decoupling (catalysis /// template activity)

‘translation’ mechanisms and genetic code

!

!

first major bottleneck: ‘proto-bioenergetic’ mechanisms !

INCREASE IN MOLECULAR AND ORGANIZATIONAL

COMPLEXITY

ORIGINS OF LIFE



[de la Escosura, Briones & Ruiz-Mirazo, Journal Systems Chemistry – forthcoming]

Biomembranes: (not just ‘hosts’ or ‘containers’ but)

SEMIPERMEBLE SUPRAMOLECULAR STRUCTURES THAT DEFINE THE BOUNDARIES OF THE SYSTEM AND ALLOW

ACTIVE CONTROL OF MATTER-ENERGY FLOW THROUGH IT (TRANSPORT + ENERGY TRANSDUCING MECHANISMS)

between boundary (scaffolding)

and protometabolic reactions

THE ‘BOTTOM-UP’ RATIONALE FOR EARLY COMPARTMENTALIZATION

‘co-evolution’

(Pre-biopolymer) scenario with: • SELF-ASSEMBLING LIPID VESICLES made of fatty acids, amphiphiles/surfactants, alcohols, mixtures,... evidence from: (a) external sources [Deamer 1986, 1997; Dworkin et al. 2001] (b) abiotic (Fischer-Tropsch) synthesis [Nooner et al. 1976; Allen & Ponnamperuma 1967; Rushdi & Simoneit 2001] • SHORT PEPTIDE CHAINS (rudimentary channels/carriers and catalysts) made of: Ala, Gly, Asp, Glu, Ser, Val… evidence from: (a) external sources [Pizzarello et al. 2006; Bernstein et al. 2002] (b) abiotic (Strecker, SIPF,… ) synthesis [Miller 1953; Rode 1999]

• VARIOUS ‘COENZYME-LIKE’ COMPOUNDS (e- carriers, pigments...) • PAHs: PHOTOCHEMICALLY ACTIVE and MEMBRANE STABILIZING!

• PRIMITIVE ENERGY TRANSDUCTION MECHANISMS ? (‘chemical and chemiosmotic’ -- energy currency precursors)

‘BOTTOM-UP’ APROACH: facing the evidence

PRODUCTION OF MOLEC. COMPLEXITY (e.g., POLYPEPTIDES)

DEVELOPMENT OF COMPARTMENTS

• avoid diffusion • adequate scaffolding to anchor

regulatory/transduction mechanisms • catalytic effect (hydrophobic phase)

• control of osmotic imbalances • accessibility of simple molecules

• constructive use of conc. gradients

Why postpone the appearance of compartments when they seem to be pivotal for the material-energetic

implementation of a complex reaction system ?? (+later on: only makes integration problems worse!)

‘COMPARTIMENTALIST VIEW’: Oparin, Morowitz, Deamer, Luisi, Harold, Monnard, Yomo, Sugawara ….

« At first glance, localization on the outer surface of vesicles (or on the surface of mineral particles, within porous rocks, etc.) would seem to pose less of a problem with respect to accessibility to oligonucleotide or activated monomer building blocks, as well as primers and divalent cations. However, if an evolving genetic system became adapted to and dependent on such an environment, the subsequent transition to a membrane based cellular structure would have been very difficult, if not impossible. Although a protocellular structure poses more problems initially, it is actually simpler to solve these problems up front rather than leave them till later when they could become completely intractable. »

[Szostak 2012, Journal of Systems Chemistry] (‘The eightfold path to non-enzymatic RNA replication’)

NATURE 2008 Jul 3; 454:122-5.

‘basic autonomous’ systems

‘OLIGOMER (peptides) WORLD’

‘hereditary autonomous’ systems

‘ONE-POLYMER (RNA) WORLD’

minimal living systems (autonomy + open-ended evolution):

‘TWO/THREE-POLYMER WORLD’ (RNA-protein/DNA-RNA-protein)

second major ‘bottleneck’: ‘template-replication’ mechanisms

third major bottleneck: phenotype-genotype decoupling (catalysis /// template activity)

‘translation’ mechanisms and genetic code

!

!

first major bottleneck: ‘proto-bioenergetic’ mechanisms !

INCREASE IN MOLECULAR AND ORGANIZATIONAL

COMPLEXITY

ORIGINS OF LIFE

FUNCTION

INFORMATION



[de la Escosura, Briones & Ruiz-Mirazo, Journal Systems Chemistry – forthcoming]

• CHEMISTRY ON AQ.-ORGANIC INTERFACES AND HETEROGENOUS ENVIRONMENTS (e.g., colloids, supramolecular structures)

TO OVERCOME -partially, at least-THERMODYNAMIC HURDLES AND GAIN FURTHER UNDERSTANDING ABOUT THE DEVELOPMENT OF SPATIAL CONTROL (selective diffusion/transport through boundaries)

• PUSH THE FIELD OF ORGANOCATALYSIS BUT WITH THE AIMTO GAIN FURTHER UNDERSTANDING ABOUT THE DEVELOPMENT OF KINETIC CONTROL (theory on the origins of enzyme catalysis ?)

• EXPLORE DIVERSE MIXTURES OF BIO-MOLECULAR PRECURSORS TO ACHIEVE A ROBUST AND AUTONOMOUS ENGAGEMENT OF

SYNTHETIC PATHWAYS (‘ORGANIC SYSTEMS CHEMISTRY’) & FUNCTIONAL COUPLINGS and INTEGRATION (‘INFRA-BIOLOGY’)

• EVOLUTIONARY BOTTLENECKS: origin of GENETIC MECHANISMS - Templates leading to RNA-worlds (embedded in protocells) - Phenotype-genotype decoupling and genetic code

• NEW TOOLS for the CHALLENGE: DCCs, nano- and micro-FLUIDICs, high-throughput techniques in vitro evolution, massive-NMR,…

[Singer and Nicholson’s (1972) ‘fluid-mosaic’ model -- Edidin 2003]

[LIPID DIVERSITY !]

modern (complex) cellular boundaries

protocell (?)

vesicles from simple amphiphiles

‘TOP-DOWN’ main problems:

‘BOTTOM-UP’ main problems:

ORIGIN OF BIOMEMBRANES: ‘BOTTOM-UP/TOP-DOWN’ APPROACHES

high molecular complexity ‘lipid divide’

low permeability

low stability (pH, ionic strength) high cvc values

500 nm

SIMPLE CHEMISTRY SELF-ASSEMBLY

SELF-ASSEMBLY

L L X

SIMPLE CHEMISTRY

SELF-ASSEMBLY

L

Z

Z’

SIMPLE CHEMISTRY

SELF-ASSEMBLY

L

Y

Y+A

B W

SIMPLE CHEMISTRY

Two-lipid membranes: FROM ‘SELF-ASSEMBLY’ TO ‘SELF-PRODUCTION’

[Piedrafita et al. ECAL 2009; --- Ruiz-Mirazo et al. 2011 AEMB, Springer Series]

unpublished results [Piedrafita 2013 – PhD Thesis]



[Shirt-Ediss et al. 2014 – Scientific Reports 4, 5675 --doi: 10.1038/srep05675]



[Shirt-Ediss et al. 2014 – Sci. Rep. 4, 5675]



[Shirt-Ediss et al. 2014 – Scientific Reports]

[Mavelli & Ruiz-Mirazo 2013 – Integr. Biol. 5, 324-341 -- doi: 10.1039/c2ib20222k]

≥ 1.85

‘AREA-DOUBLING’ TIME

‘HYDRAULIC PERMEABILITY’

‘BENDING MODULUS’

‘SPONTANEOUS MEMBRANE CURVATURE’

[Bozic & Svetina 2004]

‘self-production’ [minimal sense] regular cycles of ‘self-re-production’! (KINETIC CONDITIONS?)

?

1 1 g

g g g

S dVdV dSV dt S dt V dS

γ

= =

3 2g g g

dV dS dRV S R

= =

GEOMETRIC CHARACTERIZATION OF

GROWTH AND REPRODUCTION REGIMES

1 11.0g g

dV dSV dt S dt

γ

= ⇔ =

Condition for stationary reproduction

γ: ‘GROWTH CONTROL COEFFICIENT’

1 1 g

g g g

S dVdV dSV dt S dt V dS

γ

= =

DERIVING THE S-V SYNCHRONIZATION

CONDITION FOR STATIONARY REPRODUCTION 1 11.0

g g

dV dSV dt S dt

γ

= ⇔ =

[ ]( ) [ ]( )2L

in out L in out LEnv

dS k S L k n k S L k ndt

α = − + −

[ ]( ) [ ]( ) 0in out L in out LEnv Eqk S L k n k S L k n− ≈ − = CLOSE TO

EQUILIBRIUM

[ ]2

Lin

dS k S Ldt

α= ∆

[ ][ ] [ ] [ ]coreL upt L in

A

d L L dV S L dVv v v k Ldt V dt N V V dt

= − − = − ∆ − [ ] [ ] [ ]A AL L Eq

in in

N NdV dVL v V L v V Lk S dt k S dt

∆ = − ≈ −

[ ] AL

in

N VL vk S

∆ ≈

2L

A LdS N V vdt

α ≈

[ ] [ ]( )SpeciesReactions1 1

i i i LT Envi

dV Sm r X X vV dt C Vρ ρ

ρ

= ∆ + ℘ − −

∑ ∑

[ ] [ ]( )SpeciesReactionsT T

i i i LEnvi

dC S C dVm r X X vdt V V dtρ ρ

ρ

= ∆ + ℘ − − −∑ ∑( )T Taq aq Env

dV S C Cdt

ω= ℘ −

((νupt ~ νL))

Stano et al. 2006

Zhu & Szostak. 2009

Baumgart et al. 2003 Takakura et al. 2003

Question: ‘RELIABLE REPRODUCTION’ IN PROTOCELLS WITHOUT TEMPLATES OR A COMPLEX METABOLISM ???

«If relationships become too complex, conceptual expression may well be the most appropriate way of formulating certain aspects of the theory --- and, given the inhomogeneity of many classes of biology, conceptual language may frequently be the most suitable and appropriate means of expressing the basic relationships pertaining to the regularities of biological theory. »

[Walter M. Elsasser (1966)]

Thank you! Acknowledgments (experiments): Acknowledgments

(theoretical modeling):

Acknowledgments (conceptual):

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